Nigella sativa L. (black seed) is one of the main medicinal plants frequently cited in traditional Persian medicine manuscripts for management of acne vulgaris. The present study was designed to investigate the efficacy of a topical preparation from N. sativa in acne vulgaris. In a randomized double-blind controlled clinical trial, 60 patients (30 patients in treatment and 30 in placebo group) were randomly received N. sativa hydrogel (standardized based on thymoquinone) or placebo hydrogel, twice daily for 60 days. The Investigator's Global Assessment (IGA) grading score was recorded for each patient. Moreover, acne disability index (ADI) was evaluated using a standard questionnaire filled out by the patients at the beginning and end of the study. A 78% mean reduction in the IGA score on the N. sativa-treated group was recorded compared with 3.3% on the vehicle-treated one. Significant reductions in the number of comedones, papules, and pustules were observed in the treatment group compared with placebo after 2 months. Also, ADI was decreased 63.49% in the treatment versus 4.5% in the placebo groups. No adverse event was recorded. N. sativa hydrogel had significant effects on improving the symptoms of acne vulgaris with acceptable tolerability.